Systems Biology Research Group

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cobradbcobradbPublic
COBRAdb loads genome-scale metabolic models and genome annotations into a relational database. It already powers BiGG Models, and it is available under the MIT license.
Python 20 13
ssbiossbioPublic
A Python framework for structural systems biology
Python 107 28
cobramecobramePublic
A COBRApy extension for genome-scale models of metabolism and expression (ME-models)
Python 36 17
ecolimeecolimePublic
Data and tools necessary to construct iJL1678b-ME, a genome-scale model of E. coli K-12 MG1655 metabolism and expression
Python 4 12
bigg_modelsbigg_modelsPublic
The BiGG Models website server
Python 81 18
precise-dbprecise-dbPublic
A high-fidelity E. coli RNA-seq compendium
Jupyter Notebook 32 19

Repositories

Showing 10 of 80 repositories

pyphylon Public
Python package for analyzing and visualizing co-occuring gene / allele sets (phylons) within a pangenome
SBRG/pyphylon’s past year of commit activity
Python 1MIT 1 6 2 UpdatedMar 13, 2025
pymodulon Public
Python package for analyzing and visualizing iModulons
SBRG/pymodulon’s past year of commit activity
Python 12MIT 14 9 (2 issues need help) 3 UpdatedMar 3, 2025
PromoterModeling Public
Sequence-based ML models of gene regulation
SBRG/PromoterModeling’s past year of commit activity
Jupyter Notebook 1MIT 1 0 0 UpdatedFeb 8, 2025
PMkbase Public
All code files for PMkbase.com
SBRG/PMkbase’s past year of commit activity
HTML0MIT0 0 0 UpdatedJan 25, 2025
Bacterial_TRN_Dominance_and_Independence Public
Repository for manuscript 'Dominance and Independence within Bacterial Transcriptional Regulation'
SBRG/Bacterial_TRN_Dominance_and_Independence’s past year of commit activity
Jupyter Notebook 1MIT0 0 0 UpdatedJan 21, 2025
iModulonMiner Public Forked fromavsastry/modulome-workflow
Workflow to download, process, and explore microbial RNA-seq data from NCBI SRA
SBRG/iModulonMiner’s past year of commit activity
HTML 10MIT 24 4 2 UpdatedNov 7, 2024
PM_Activity_Calls Public
Python notebook workflow to make metabolic activity calls on PM samples
SBRG/PM_Activity_Calls’s past year of commit activity
Jupyter Notebook0MIT0 0 0 UpdatedSep 18, 2024
ElectricColi Public
Modeling and data analysis code for the E. coli extracellular electron transfer project
SBRG/ElectricColi’s past year of commit activity
Jupyter Notebook0MIT0 0 0 UpdatedJun 29, 2024
GDS-Public Public
SBRG/GDS-Public’s past year of commit activity
Jupyter Notebook0MIT0 0 0 UpdatedMay 8, 2024
noncoding_alleleome Public
SBRG/noncoding_alleleome’s past year of commit activity
Jupyter Notebook 2MIT0 0 0 UpdatedApr 16, 2024